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Tutorials

I. Architecture of HLASSB_DB
II. HLA Class I supertypes and alleles includes in HLASSB_DB
III. Usage of HLASSB_DB
    i. Seach for peptides cross-binding to the HLA molecules in the same supertype
    ii. Browse the supertype-specific HLA classI-binding data by source species and protein
    iii. Search for HLA supertype-specific binding peptides by protein sequence
    iv. Search for mutated analogues of an input peptide
    v. Search for promiscuous peptides binding to alleles across HLA class I supertypes

Architecture of HLASSB_DB

HLA Class I supertypes and alleles includes in HLASSB_DB

Ref: Sidney J, Peters B, Frahm N, Brander C, Sette A. HLA class I supertypes: a revised and updated classification. BMC Immunol. 2008 Jan 22;9:1


Usage of HLASSB_DB

Seach for peptides cross-binding to the HLA molecules in the same supertype

"Input a peptide sequence": amino acid sequence coding with uppercase letters. example : "FLPSDFFPSV"
"Browe the peptide by supertype": 10 HLA supertype A1, A2, A3, A24, B7, B44, B27, B8, B26 and B56 are available.
Once a supertype was selected, the corresponding alleles belonging to this supertype were given. Users could choose at most five alleles to defined their query for peptides that can bind or not to these alleles. Users also could search the supertype specific binding peptide from specific species by "select the source species". Such as "Hepatitis B virus","Influenza B virus" et.al.
In the output result, the "N "represents the non-binding peptide, while the "P"represents the binding peptide.


Browse the supertype-specific HLA classI-binding data by source species and protein

Browse the supertype-specific HLA classI-binding data by source species and protein, Once the source species was selected the corresponding proteins included in HLASSB_DB was shown, and the users could selected the protein name in "Browse the peptides by source protein".


Search for HLA supertype-specific binding peptides by protein sequence

Search for HLA supertype-specific binding peptides by protein sequence, the protein name could give an arbitrary name. The protein sequence should be a plain sequence. Such as:
MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTASALYREALESPEHCSPHHTALRQAILCWGELMTLATWVGVNLED
PASRDLVVSYVNTNMGLKFRQLLWFHISCLTFGRETVIEYLVSFGVWIRTPPAYRPPNAPILSTLPETTVVRRRGRSP
RRRTPSPRRRRSQSPRRRRSQSRESQC


Search for mutated analogues of an input peptide

Search for mutated analogues of an input peptide, amino acid sequence coding with uppercase letters. example : "FLPSDFFPSV".
Options:
"subsequence" Searching peptides that including the input sequence
"mutated analogues", Searching the mutated analogues of input sequence, here the analogues were defined as peptide that had no more than two different amino acid from the input sequence.


Search for promiscuous peptides binding to alleles across HLA class I supertypes

Search for promiscuous peptides binding to alleles across HLA class I supertypes, user should select at least two different supertypes.



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